I-TASSER results

I-TASSER results for job id Rv2376c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (168 residues)
MKMVKSIAAGLTAAAAIGAAAAGVTSIMAGGPVVYQMQPVVFGAPLPLDPASAPDVPTAA
QLTSLLNSLADPNVSFANKGSLVEGGIGGTEARIADHKLKKAAEHGDLPLSFSVTNIQPA
AAGSATADVSVSGPKLSSPVTQNVTFVNQGGWMLSRASAMELLQAAGN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MKMVKSIAAGLTAAAAIGAAAAGVTSIMAGGPVVYQMQPVVFGAPLPLDPASAPDVPTAAQLTSLLNSLADPNVSFANKGSLVEGGIGGTEARIADHKLKKAAEHGDLPLSFSVTNIQPAAAGSATADVSVSGPKLSSPVTQNVTFVNQGGWMLSRASAMELLQAAGN
Prediction	CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEHCCCCCCCCCEEEEEEEEHCCCCCCCCCCCEEEEHCCCEEEEHHHHHHHHHHHCC
Conf.Score	986466999999999998555678888899988777667778899998999989999999999999999899999878776544799875478999999999985999879998587788897799999998689988876768999699668748899999999779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MKMVKSIAAGLTAAAAIGAAAAGVTSIMAGGPVVYQMQPVVFGAPLPLDPASAPDVPTAAQLTSLLNSLADPNVSFANKGSLVEGGIGGTEARIADHKLKKAAEHGDLPLSFSVTNIQPAAAGSATADVSVSGPKLSSPVTQNVTFVNQGGWMLSRASAMELLQAAGN
Prediction	754344130321210111121222433566543344344443635345644556732426302500440344714364314203323466334213410532474461414040550546564403030203137464443431312374314113520230143358
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. (Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60                  80                 100                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEHCCCCCCCCCEEEEEEEEHCCCCCCCCCCCEEEEHCCCEEEEHHHHHHHHHHHCC
MKMVKSIAAGLTAAAAIGAAAAGVTSIMAGGPVVYQMQPVVFGAPLPLDPASAPDVPTAAQLTSLLNSLADPNVSFANKGSLVEGGIGGTEARIADHKLKKAAEHGDLPLSFSVTNIQPAAAGSATADVSVSGPKLSSPVTQNVTFVNQGGWMLSRASAMELLQAAGN

4ke2A

0.13

1.00

0.81

MUSTER

MNIDRAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVS

2rrlA

0.10

0.08

0.79

0.55

dPPAS

--------------------HMASDDRATGPALTPLVVAAAATSAKVEVDSPPAPVTHGAAMPTLSSATAQPLPVASAPVLSAPLGSHEWQQTFSQQVMLFTRQGQQ---SAQLR-LHPEELGQVHISLKLDDNQA------QLQMVSPHS-----HVRAALEAALPM

4i4kA

0.13

0.08

0.66

0.68

wdPPAS

----------------------------------------------STDSITSAPDAALAAVAALPARIVA-DHDADRFADVLPGLFRKGRENIRTHAAAFAGPYKGTRVIGSPIDARLLGDGLLITEGGILAPGETEASGDGLAVEQDGQWRLA----------AYQ

4pscA

0.15

0.14

0.97

0.68

wMUSTER

INEFLSELAKVMPIGDTITAACDLISDGEDAAASLFGISETENDPCGDCDPGNVGVLVGPWFFDSLQTALGSRVPYPASVQDFLSGSVQNGINMANQIKSVLQSCPNTKLVLGG-NLDAATMSKISAVVLFGDPYYGKPVANFLVV--QGG--LTDTAAAFVVPLVSH

2gqbA

0.15

0.10

0.65

0.80

wPPAS

MSIFGKIMSAIF-------------DSAAASPGGAQAPATTGAAGTAPTAPQPTAAPSI-DVAPILDKAVKAKGE---RTSIVDDSSLSARKELAKEL------------------YSGDMNDSASMNI----------------------W-LHKQVMSKLVANGGK

2m5yA

0.14

0.08

0.60

0.91

dPPAS2

----------------------GSSPNSEDDSSAISTMTTTTAAPTSTSVKPAAPRAEAARTADRLKAAGLPDVAA----TTVYYTEVEGERATADAVGRTLG----AAVELRLPELSDQPPGVIVVVTG--------------------------------------

4ke2A

0.13

0.99

0.83

PPAS

MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNA-AAAKAAAVATAVSDAAATAATAAAVAAATLEAA

1mwrB1

0.15

0.09

0.60

0.89

Env-PPAS

----------------------------------------------------------DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVET-ERPIKIYNSLGVKDINIQDRKIKKR----VDAQYKIKTNYGNIDRNVQFNFVKEDGWKLDWDHSVII---PG-

5cwdA

0.13

0.12

0.93

0.71

MUSTER

EKAARKAAESDEEVAKQAAKDCLEVAKQAGMPTKEAARSFCEAAARAAAESNDEEV-AKIAAKACLEVAKQAGMPTKEAARSFCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAKRAAKESNDEEVE----------KIAKKACKEVAKQAGM

3lmmD1

0.12

0.10

0.83

0.54

dPPAS

--EGRREQLIAQVESILASAADGRVQKTKETQSVDFKEEAGRRNGPQIEPGKPENPEAADKLADEVACANTPGVGIEDKTGRIIGTELD-----IDWLRQGIFTRIDVAPDVVAKRV----LGQRVLAIYVAAAAEPIEDTSDRLRWRVGD-----------------

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=-4.01

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.6±3.7Å

Download Model 2

C-score=-2.85

Download Model 3

C-score=-4.37

Download Model 4

C-score=-4.47

Download Model 5

C-score=-4.74

Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	5jmdA	0.474	5.32	0.031	0.839
2	4mmhA2	0.474	5.38	0.041	0.827
3	4a01A	0.471	5.21	0.054	0.845
4	4fnvA2	0.467	5.35	0.048	0.816
5	3a0oA	0.467	5.33	0.067	0.821
6	2gbwB	0.464	4.02	0.043	0.667
7	1n7qA	0.464	5.30	0.049	0.809
8	2p0mA	0.463	5.47	0.076	0.827
9	2wdaA	0.463	5.29	0.042	0.798
10	1wqlB	0.461	4.10	0.033	0.655

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.06	5	3jupA	AKD	Rep, Mult	94,102,110,112,142
2	0.06	5	3ophA	MA4	Rep, Mult	68,115,125,155,158,159
3	0.04	3	1w5cB	CLA	Rep, Mult	92,99
4	0.04	3	2p0mB	RS7	Rep, Mult	61,65,68,78,82
5	0.04	3	2bmo0	III	Rep, Mult	60,64,67,68,71,79,80,98,105,109,111,112,113,114,115,128,130,132
6	0.04	3	4stdC	BFS	Rep, Mult	62,69,125,127,129,144,146,148,153,163
7	0.02	2	1c1wL	ZN	Rep, Mult	71,79
8	0.02	2	1xk0A	NO	Rep, Mult	102,106
9	0.02	2	3juqA	AJD	Rep, Mult	73,95,98,99,102,107,142,161
10	0.02	2	2j4eC	MG	Rep, Mult	82,84
11	0.01	1	3a52A	MG	Rep, Mult	26,27
12	0.01	1	4v1fA	BQ1	Rep, Mult	13,14,17
13	0.01	1	3a9qR	CA	Rep, Mult	100,104
14	0.01	1	5stdB	UNN	Rep, Mult	69,94,95,102,128,130,132,141,143,145
15	0.01	1	1n47A	UUU	Rep, Mult	72,73
16	0.01	1	2wilA	UUU	Rep, Mult	113,116
17	0.01	1	3zvwC	MG	Rep, Mult	139,140
18	0.01	1	4xk8i	CLA	Rep, Mult	157,160
19	0.01	1	3b4pB	3B4	Rep, Mult	94,97,98,102,109
20	0.01	1	3prqJ	III	Rep, Mult	152,160

	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.060	1o7hB	0.450	4.01	0.097	0.643	1.14.12.12	77
2	0.060	3ig5A	0.431	4.94	0.042	0.708	6.3.2.2	NA
3	0.060	2iukB	0.469	5.53	0.050	0.845	1.13.11.12	NA
4	0.060	1u60C	0.430	4.91	0.072	0.714	3.5.1.2	86,89,92
5	0.060	1j0mA	0.458	5.47	0.068	0.821	4.2.2.12	NA
6	0.060	2e9bA	0.430	4.87	0.084	0.702	3.2.1.41	NA
7	0.060	3d3lA	0.459	5.37	0.089	0.816	1.13.11.31	NA
8	0.060	2p0mB	0.309	6.30	0.055	0.643	1.13.11.33	65,69,85
9	0.060	1qh1B	0.432	5.29	0.034	0.756	1.18.6.1	57
10	0.060	1e3vB	0.428	4.34	0.036	0.649	5.3.3.1	NA
11	0.060	1n2cB	0.439	5.14	0.060	0.756	1.18.6.1	NA
12	0.060	2ux0A	0.423	4.35	0.061	0.631	2.7.11.17	86,141,154
13	0.060	4stdA	0.458	4.12	0.060	0.679	4.2.1.94	NA
14	0.060	3gzxB	0.457	3.73	0.078	0.631	1.14.12.18	77
15	0.060	1no3A	0.455	5.52	0.038	0.851	1.13.11.12	NA
16	0.060	2p0mA	0.463	5.47	0.076	0.827	1.13.11.33	NA
17	0.060	2q1fA	0.457	5.61	0.074	0.833	4.2.2.21	NA
18	0.060	1iexA	0.438	5.17	0.073	0.768	3.2.1.58	NA
19	0.060	1nu3B	0.423	3.91	0.047	0.595	3.3.2.8	NA

(a)	Cscore^EC is the confidence score for the EC number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.06	0.473	5.33	0.08	0.83	3aflA	GO:0016829
1	0.06	0.336	5.84	0.07	0.66	3tx1A	GO:0003824 GO:0005737 GO:0007049 GO:0008360 GO:0008762 GO:0009252 GO:0016491 GO:0016614 GO:0050660 GO:0051301 GO:0055114 GO:0071555
2	0.06	0.374	5.73	0.05	0.71	4rdtA	GO:0004872 GO:0006810 GO:0009279 GO:0016020 GO:0016021
3	0.06	0.419	5.42	0.07	0.76	1hn0A	GO:0003824 GO:0005576 GO:0005975 GO:0016829 GO:0016837 GO:0030246 GO:0034000 GO:0042597 GO:0046872
4	0.06	0.352	4.38	0.09	0.55	4gdzA	GO:0046872
5	0.06	0.293	6.08	0.04	0.58	3plaE	GO:0000494 GO:0003723 GO:0006364 GO:0008033 GO:0008168 GO:0008649 GO:0016740 GO:0031167 GO:0031428 GO:0032040 GO:0032259 GO:1990258 GO:1990259
6	0.06	0.377	5.77	0.05	0.73	4rvwA	GO:0004872 GO:0006810 GO:0009279 GO:0016020 GO:0016021
7	0.06	0.343	6.45	0.04	0.73	1ytmA	GO:0000166 GO:0004611 GO:0004612 GO:0005524 GO:0005737 GO:0006094 GO:0016829 GO:0016831 GO:0017076 GO:0046872
8	0.06	0.281	5.81	0.03	0.55	3my0K	GO:0000166 GO:0001525 GO:0001701 GO:0001936 GO:0001937 GO:0001938 GO:0001946 GO:0001955 GO:0001974 GO:0002043 GO:0004672 GO:0004674 GO:0004675 GO:0004702 GO:0005024 GO:0005025 GO:0005524 GO:0005886 GO:0005887 GO:0006275 GO:0006355 GO:0006468 GO:0007162 GO:0007165 GO:0007178 GO:0007179 GO:0008015 GO:0008217 GO:0008285 GO:0009986 GO:0010596 GO:0010862 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016361 GO:0016740 GO:0019901 GO:0023014 GO:0030308 GO:0030336 GO:0030425 GO:0030509 GO:0030513 GO:0032332 GO:0032924 GO:0035313 GO:0043025 GO:0043535 GO:0043537 GO:0045602 GO:0045603 GO:0045766 GO:0045893 GO:0045944 GO:0046332 GO:0046872 GO:0048185 GO:0048514 GO:0050431 GO:0051291 GO:0051895 GO:0060836 GO:0060840 GO:0060841 GO:0061154 GO:0061298 GO:0071560 GO:0071773 GO:0098821 GO:2000279
9	0.06	0.317	6.09	0.06	0.64	1ewyA	GO:0004324 GO:0009579 GO:0016020 GO:0016491 GO:0030089 GO:0042651 GO:0050660 GO:0050661 GO:0055114
10	0.06	0.474	5.32	0.03	0.84	5jmdA	GO:0016829 GO:0042597
11	0.06	0.343	5.87	0.05	0.67	4pabB	GO:0005542 GO:0005739 GO:0006579 GO:0016491 GO:0019695 GO:0035999 GO:0042426 GO:0047865 GO:0050660 GO:0055114
12	0.06	0.455	5.28	0.05	0.82	4ojzA	GO:0000272 GO:0005975 GO:0016829 GO:0042597 GO:0046872
13	0.06	0.362	5.38	0.07	0.64	2f8jA	GO:0000105 GO:0003824 GO:0004400 GO:0008152 GO:0008483 GO:0008652 GO:0009058 GO:0016740 GO:0030170 GO:0080130
14	0.06	0.241	4.72	0.08	0.40	2kq2A	GO:0003676 GO:0004523 GO:0090502
15	0.06	0.459	5.42	0.06	0.83	5jmfA	GO:0016829 GO:0042597
16	0.06	0.471	5.32	0.05	0.83	4mmhA	GO:0015021 GO:0016829 GO:0030200 GO:0042597
17	0.06	0.280	5.14	0.03	0.47	4umsA	GO:0000272 GO:0005179 GO:0005576 GO:0030246
18	0.06	0.265	4.63	0.05	0.43	2ju5A	GO:0016491 GO:0042597 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0034000	GO:0004872	GO:0008762	GO:0030246	GO:0050660
GO-Score	0.12	0.06	0.06	0.06	0.06	0.06
Biological Processes	GO:0008360	GO:0006810	GO:0055114	GO:0005975	GO:0051301	GO:0071555	GO:0007049	GO:0009252
GO-Score	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06
Cellular Component	GO:0005576	GO:0016021	GO:0009279	GO:0005737	GO:0042597
GO-Score	0.06	0.06	0.06	0.06	0.06

(a)	Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)	The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.